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idba_hybrid - Online in the Cloud

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This is the command idba_hybrid that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


idba_hybrid - Iterative de Bruijn Graph Assembler for hybrid sequencing data

SYNOPSIS


idba_hybrid -r read.fa -o output_dir [--reference ref.fa]

DESCRIPTION


IDBA-Tran is an iterative De Bruijn Graph De Novo short read assembler for transcriptome.
It is purely de novo assembler based on only RNA sequencing reads. IDBA-Tran uses local
assembly to reconstructing missing k-mers in low-expressed transcripts and then employs
progressive cutoff on contigs to separate the graph into components. Each component
corresponds to one gene in most cases and contains not many transcripts. A heuristic
algorithm based on pair-end reads is then used to find the isoforms.

OPTIONS


-o, --out arg (=out)
output directory

-r, --read arg
fasta read file (<=128)

--read_level_2 arg
paired-end reads fasta for second level scaffolds

--read_level_3 arg
paired-end reads fasta for third level scaffolds

--read_level_4 arg
paired-end reads fasta for fourth level scaffolds

--read_level_5 arg
paired-end reads fasta for fifth level scaffolds

-l, --long_read arg
fasta long read file (>128)

--reference arg
reference genome

--mink arg (=20)
minimum k value (<=124)

--maxk arg (=100)
maximum k value (<=124)

--step arg (=20)
increment of k-mer of each iteration

--inner_mink arg (=10)
inner minimum k value

--inner_step arg (=5)
inner increment of k-mer

--prefix arg (=3)
prefix length used to build sub k-mer table

--min_count arg (=2)
minimum multiplicity for filtering k-mer when building the graph

--min_support arg (=1)
minimum supoort in each iteration

--num_threads arg (=0)
number of threads

--seed_kmer arg (=30)
seed kmer size for alignment

--min_contig arg (=200)
minimum size of contig

--min_region arg (=500)
minimum size of region in reference genome

--similar arg (=0.95)
similarity for alignment

--max_mismatch arg (=3)
max mismatch of error correction

--min_pairs arg (=3)
minimum number of pairs

--max_gap arg (=50)
maximum gap in reference

--no_local
do not use local assembly

--no_coverage
do not iterate on coverage

--no_correct
do not do correction

--pre_correction
perform pre-correction before assembly

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